December 2010

Science Focus: Ajit Varki

A look at ASBMB member Ajit Varki and how he uses his research on the biochemistry, molecular biology and genetics of sialic acids to answer broader questions about human origins, disease and evolution. (Titled "Science of Sialic Acids" in print version.)

Ajit VarkiIt’s not uncommon for scientists to shift their research focus in new and different directions during the course of their careers, whether to separate themselves from their mentors or to follow up on unexpected discoveries, which sometimes results in unusual research trajectories.

Even so, in 1975, when Ajit Varki first set foot on U.S. soil to pursue his interests in hematology research, he couldn’t possibly have envisioned that someday he would be taking a sabbatical at the Yerkes National Primate Research Center to learn about chimpanzees or requesting fossil samples of Neanderthals while at the same time emerging as a leading expert in glycobiology. He also never imagined that his work would be recognized by such honors as election to the American Academy of Arts and Sciences and the Institute of Medicine of the National Academies. 

But it’s a journey Varki is thrilled to have made. Currently a distinguished professor in the departments of medicine and cellular and molecular medicine at the University of California, San Diego, as well as co-director of both the UCSD/Salk Center for Academic Research and Training in Anthropogeny and the Glycobiology Research and Training Center, Varki studies the biochemistry, molecular biology and genetics of sialic acids, a diverse family of glycans, while using that information to answer broader questions about human origins, disease and evolution.

“I could not have written a better script for myself,” he says. “I can keep doing basic research in the ASBMB mold but also apply that to answer philosophical questions like, ‘What makes a human a human?’ while studying the implications for human disease.”

Unconventional Origins

Ajit Varki, whose own origins trace to Kerala in southwest India (along the fabled spice coast that Columbus was trying to reach in his journeys), recalls wanting to be a physician from a very early age; thus, he developed strong academic interests, particularly in biology. “Having two rather famous grandfathers (Pothan Joseph, a renowned Indian journalist and newspaper editor, and A. M. Varki, who founded one of Southern India’s first English-medium colleges) greatly raised the stakes on performance expectations in my childhood, though generally in a positive way,” he says.

The positive reinforcement helped, driving him to be the top student from Bishop Cotton Boys’ School Bangalore, often called the “Eton of the East,” and from Christian Medical College at Vellore, one of the leading medical schools in India. “Although my first love was medicine and I even spent a year working at a small rural hospital after graduation, my exposure to scientific research at CMC convinced me to try a career as a physician-scientist,” he says. However, India’s research infrastructure was not as well developed— Varki says he was fortunate to attend one of the few Indian schools that blended research, science and medicine— and he knew he had to leave the country to pursue further research training.

Ajit Varki discusses research with postdoctoral fellow Oliver Pearce.

“It’s much different today in India,” says Varki, who returns to his native country each year to serve as a visiting professor at the  Indian Institute of Technology Madras and to help enhance academic excellence at CMC. “The government has invested heavily in R&D, and new research institutes are now springing up everywhere.”

But back then, the one country where physicians seemed to conduct research on par with doctorates was in the United States. So Varki arrived stateside, like many before and since, with a suitcase, $6.00 in his pocket and a dream (in his case, doing great research).

“Now, I knew my research opportunities would improve if I first finished my medical training,” he says. “But despite having been the number one student throughout my schooling, I could not even get an interview at any major university; at that time in the 1970s, there was a good deal of prejudice against foreign doctors,” he says. “Today, I get bemused whenever I get invited to present an honorific lecture at some of these institutions and think back to when they wouldn’t even talk to me.”

So Varki had to claw his way up the academic ladder, starting at a small community hospital in Philadelphia, then moving to the University of Nebraska and finally entering a hematology-oncology fellowship at Washington University in St. Louis.

There, he ended up joining the lab of Stuart Kornfeld. “Honestly, I didn’t know much about glycobiology (which was Kornfeld’s area of expertise), but I decided that this guy was so extremely smart and that I should go work for him.”

The timing was fortunate, as Kornfeld’s group was just making their first of many discoveries about the mannose 6-phosphate pathway, wherein mannose moieties on lysosomal enzymes are phosphorylated in the Golgi, which in turn acts as a signal to target them to the lysosome.

“It was an exciting time,” notes Varki, who identified the enzyme responsible for the second step in the two-step pathway, the phosphodiester glycosidase. “The lab was uncovering the first known biological function for the sugar in a eukaryotic system. And not only a function; we soon identified the M6P receptor and showed that I-cell disease was brought on by a deficiency of phosphotransferase, the enzyme that catalyzes the first step of the pathway.”

Spreading His Wings

In 1982, Varki completed his work with Kornfeld and joined the faculty at UCSD, where, in a move he wouldn’t advise for a young investigator today, he completely dropped all his M6P work and decided to prove himself by doing something completely different.

The question was what avenue to pick. His appointment at UCSD coincided with a national surge in molecular biology, but he made a conscious decision “not to jump on that bandwagon.” He wanted to remain in glycobiology, and given that it was an underrepresented field— and still is today, though Varki notes that increased enthusiasm among young scientists is spurring a slow but steady growth— he had plenty of options.

“I had written one paper on sialic acids with Stuart,” he says. “And I was intrigued that this family of sugars included over 50 different varieties, but no one really knew much about this diversity or its functions.”

"The question was what avenue to pick. His appointment at UCSD coincided with a national surge in molecular biology, but he made a conscious decision “not to jump on that bandwagon.”

During the next 15 years, Varki and his team set out to characterize essential features of sialic acid structure, biochemistry and biology and the connections of these molecules— which dot the surface of every cell— to infections, the immune response and cancer.

Among his many important contributions, which can be evidenced by the more than 50 Journal of Biological Chemistry articles he published during this period, he worked on O-acetylation, a tightly regulated yet poorly understood sialic acid modification, and conducted numerous studies with the receptor protein CD22, which is found on B cells and is one of several lectin-like proteins that bind to sialic acids. That led him to coin the term by which these receptors are now known— Siglecs (Sialic acid binding Ig-like Lectins)— and to define the larger family they belong to, which he called I-type lectins.

During this period, Varki also followed his journalistic heritage (his mother writes articles for newspapers and magazines in India) and became chief editor of the Journal of Clinical Investigation, shepherding it through the transition to electronic publishing and simultaneously making it the first major journal to go to full open access in 1996. More recently, he collaborated with the National Center for Biotechnology Information and Cold Spring Harbor Laboratory Press to edit the first-ever major open access textbook, the second edition of “Essentials of Glycobiology.” In both instances, he demonstrated financially viable models of free access to knowledge, something in which he ardently believes. Another cause Varki advocates for is having on-site infant care facilities for women scientists, having watched the experiences of Nissi Varki, his CMC classmate, spouse and longtime collaborator, whom he also credits greatly for any successes he has had.

In 1998, he made perhaps his signature breakthrough when he examined blood samples from humans and several ape species, including chimpanzees, for their sialic acid composition. The impetus for this project had occurred years earlier, when Varki witnessed a case of serum sickness in a patient he was treating with immunosuppressive serum therapy. Varki had assumed the response was due to an immune reaction against foreign proteins in the horse serum but then read studies suggesting that sialic acids on the proteins might be the antigen.

This seemed odd, given sialic acids’ ubiquitous presence, so he conducted a chromatographic analysis of the different primate species and found that humans alone lacked a particular sialic acid called N-glycolylneuraminic acid, or Neu5Gc. A follow-up study showed that the cause was a human-specific exon deletion/frameshift mutation in the gene for the enzyme that converts CMP-N-acetylneuraminic acid, or CMP-Neu5Ac, into CMP-Neu5Gc, rendering it inactive.

“I realized we had found the first known functionally significant genetic difference between humans and chimps,” Varki says of that moment. “One that produced a distinct structural difference with a clear biochemical readout; you could analyze any human or ape cell and identify whether it was human or not.” But remarkably, he later found that this nonhuman sialic acid could sneak back into the human body from dietary origins— something he proved by drinking a sample of Neu5Gc himself (with institutional review board permission, of course).

Proposed evolutionary scenario linking human-specific changes in sialic acid-related genes; from Varki, A. (2010). PNAS 107, 8939 – 8946.

On Human Nature

The lack of Neu5Gc turned out to be just the first of many genetic changes that have occurred in sialic acid biology during the course of human evolution, which has raised many intriguing questions. “If you compare mice and rats, you might find a couple of differences in sialic acid biology, the same if you compare different ape species,” Varki explains. “Yet, between humans and our closest relatives, chimps, we’ve already uncovered a dozen alterations, most in Siglec receptors, despite less than 60 identified genes involved in sialic acid biology.

“So, something has happened over the past few million years that really spurred a rapid evolution of these particular genes in the human lineage.”

In a recent review, Varki points out that sialic acids on the cell surface are common recognition targets by pathogens and that selective pressure by infectious agents is important. “A lot of diseases specific to humans, like falciparum malaria or cholera, are caused by pathogens that target sialic acids,” he says. “On the other hand, many other human pathogens disguise themselves by expressing surface sialic acids.”

“At the same time, human evolution is like a murder mystery,” he adds. “Each change only occurred once, so you can’t recreate the crime. And if you just use logic to deduce an answer, you may be wrong. After all, every single cell in a human is covered with sugars, and research has now shown biological roles for glycans that range from the sublime to the ridiculous. So if you mess around with sialic acid biology, you end up changing a lot of functions.”

Like any good mystery, the key, says Varki, is to follow all of the available clues to the answer. To do that requires comprehensive and comparative studies of the “sialome” (another term he coined) in humans, other living primates and fossil samples from hominid precursors using chromatography and mass-spectrometry as well as employing both “humanized” and “chimpanized” mouse models to compare functions of genes involved in sialic acid biology. And clues that many uniquely human diseases may have some basis in sialic acid changes have brought him full circle back to his roots in medicine.

Of course, sialic acids alone will not answer the question of human origins. That’s why Varki founded the Center for Academic Research and Training in Anthropogeny to provide a place where great minds and resources could be brought together to make connections and share ideas. The center is supported by the Mathers Charitable Foundation, which also was instrumental in funding Varki’s early evolution projects, for which he is extremely grateful. “I probably couldn’t have pursued my research without them, as I don’t think probing the meaning of humanity through glycobiology would be high on the NIH funding list.”

Varki hopes the efforts of CARTA and related places like the Leipzig School of Human Origins in Germany will help put human evolution in proper perspective.

“We’ve gone from the Victorian idea of humans as special creatures made in God’s image to the other end of the spectrum,” he says, where the influence of the popular press, and more recently genome sequencing, has pushed scientists to focus mostly on how humans and chimpanzees are similar.

“Humans are both remarkably similar and remarkably different from chimps,” Varki says. “And I think the latter part of that statement needs to be addressed a little more, in a comprehensive way.”


Varki, A., and Kornfeld, S. (1981) Purification and Characterization of Rat Liver a-N-acetylglucosaminyl Phosphodiesterase. J .Biol. Chem. 256, 9937 – 9943.

Varki, A., and Kornfeld, S. (1983) The Spectrum of Anionic Oligosaccharides Released by Endo-beta-N-acetylglucosaminidase H from Glycoproteins: Structural Studies and Analysis of Interactions with the Isolated Phosphomannosyl Receptor. J. Biol. Chem. 258, 2808 – 2818.

Powell, L. D., Sgroi, D., Sjoberg, E. R., Stamenkovic, I., and Varki, A. (1993) Natural Ligands of the B-cell Adhesion Molecule CD22 Carry N-linked Oligosaccharides with a2,6-Linked Sialic Acids That Are Required for Recognition. J. Biol. Chem. 268, 7019 – 7027.

Chou, H. H., Takematsu, H., Diaz, S., Iber, J., Nickerson, E., Wright, K. L., Muchmore, E. A., Nelson, D. L., Warren, S. T., and Varki, A. (1998) A Mutation in Human CMP-sialic Acid Hydroxylase Occurred after the Homo-pan Divergence. Proc. Natl. Acad. Sci. U.S.A. 95, 11751 – 11756.

Altheide, T. K., Hayakawa, T., Mikkelsen, T. S., Diaz, S., Varki, N., and Varki, A. (2006) System-wide Genomic and Biochemical Comparisons of Sialic Acid Biology among Primates and Rodents: Evidence for Two Modes of Rapid Evolution. J. Biol. Chem. 281, 25689 – 25702.

Varki, A. (2010) Uniquely Human Evolution of Sialic Acid Genetics and Biology. Proc. Natl. Acad. Sci. U.S.A. 107, 8939 – 8946.

Nick Zagorski ( is a science writer at ASBMB.

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